Artificial Life: Biochemical Life and Limits

On biochemical life and its limits. March 1995 — the earliest surviving piece.

Edit History: First and only edit March 6th 1995 by Andy Hook

To understand how to create an artificial primordial soup within which self-replication could boot-strap itself, and within which many orders of emergence might be seen, it may be useful to look at some of the foundations of biochemical life. Elsewhere I hope to examine the ways atoms were evolved and the tendency of the universe towards complexity. The information here is largely cobbled from John Postgate and "The Outer Reaches of Life", as well as some school texts. It is extremely brief, and is designed to serve as merely a placeholder, a reminder of basic facts.

Atoms

Our Universe consists of 92 basic elements, of which the first 4 account for 95 percent of content of life. Atoms bond by

1. covalence (lego block strategy), this is the strategy used for H2 and H2O as well.
1. Ionic bond, where one atom gives up an electron to another. Carbon; by bonding with so many things, and itself is the literal 'backbone' of life.

Catalysts moderate chemical reactions. In life catalysts are imbedded in enzymes; the enyzme has a shape to fit a target compound; it distorts the target when keyed with it and exposes part of it to the catalyst thus promoting a breakdown in the compound. Glucose for example with oxygen becomes carbon dioxide + water + ATP. ATP is a simple energy rich molecule with a bit of potassium in it. Cells use ATP by breaking last phosphate bond of ATP. Used up ATP is called ADP. Mitochondria fix ADP by burning sugar and restoring last phosphate bond.

Life itself

Earth life is based on the idea of a cell which divides the "inside" from the "outside" - often both of which are fairly stable environments - the inside being immediately controlled by the cell. Cell walls are made up of fatty strings/lipids which are semi-permeable by various chemicals under the cell's discretion (proteins form little controllable doors in the lipid wall). The wall keeps internals internal and lets nutrients in.

Early life is probably similar to the life inside the cell wall; life probably existed in a stable environment like this. Presumably inside the cell wall are simpler entities which are alive by themselves, so it isn't the cell itself I'm ultimately interested in ultimately, but some simpler life form swimming in the homeostatic soup of the cells protoplasm (organelles).

Temperature Limits

Cell wall activity is disrupted if the temperature changes from levels expressed in cell genetics.

In the cell is a water dissolved mixture of large delicate molecules called proteins. Proteins are made up of strings of amino-acids, which in turn are strings of carbon, hydrogen, oxygen, nitrogen, sulpher. There are 20 kinds of amino acids and infinite variety of proteins consisting of various kinds of amino-acids stuck together.

Protein logic is encoded into the three dimensional folding pattern of its chemical string. Overheating a protein will unravel the string thus disrupting the information and use of that information. An egg is a large cell, when an egg is boiled its proteins unravel and become opaque. Some cells can deploy heat-shock proteins which scaffold other proteins and allow more temperature tolerance (called chaperions...). Note that overheating the cell can "melt" the fatty lipid cell wall as well. There is a low temperature cyroprotectant as well but the goal here is to prevent water from becoming ice-crystals and rupturing the cell wall; presumably the proteins aren't affected by freezing.

pH Limits

Disruption also occurs if the pH relationship between inside and outside changes. Also if the internal pH changes.

On earth water is composed of 'flickering clusters of HO and H pieces' [Hofstader]. When water is acidic there are more H pieces available, when water is base there are more HO pieces available. Presumably most kinds of liquids have this kind of behaviour?

Cells have water pumped through them to extract nutrients and eliminate waste. Substances in water generate osmotic pressure across the cell wall, by regulating the internal pH the cell controls the water flow. Cells typically want a slight influx always; if the outside is too saline then the osmotic pressure is greater than the cell can muster and the cell dehydrates and is permanently disrupted. Some cells switch to potassium ions from sodium ions internally to change the pressure and create glycerol which takes the place of water but isn't susceptible to osmotic pressure - although it requires a further special mechanism to discriminate glycerol and hold onto it.

Pressure Limits

Cells are largely immune to hydrostatic pressure.

Energy Limits

Cells run on a substance called ATP. Apparently they burn organic or inorganic food with oxygen (Plants also do photosynthesis which makes organics). Energy from burning food is cached into ATP (adenosine triphosphate). Cells have "enzymes" which make ATP and those to decompose it. Energy can be released as heat or work or light.

There are six ways to make ATP, here is one method:

"Cells decompose molecules of sugar making a bit of heat and ATP. Then the sugar is further broken down into carbon dioxide (the hydrogen atoms are removed by enzymes which leaves carbon and oxygen making carbon dioxide). Oxygen gas interacts with hydrogen to make water and heat; the heat is tapped off to make ATP using special compounds and proteins."

Another way is just the first part of the above; split a sugar in two, the energy there can be used to make ATP. This is like fermentation, also if taken further some hydrogen is given off, so this explains methane belching compost on the bottom of swamps; and the anerobes in cattle that process their starchy grasses.

Anerobes are probably closer to original life than oxygen respirators.

Other Structural Issues

Proteins, lipids, carbohydrates, nucleic acid, water and salts.

Endplasmic rectilum of tubes run through the protoplasm connecting to nucleus. These transport and store stuff.

Ribosomes make proteins. Golgi apparatus package proteins for export from cell. Lysome has digestive enzymes which break down matter, lysome can also move to cell wall and eject waste. Mitochondria produces ATP - in fact seems to be independant. Microtubules can move and help sort chromosones in cell division. Microfilaments can make caterpillaring feet for moving along walls.

Note that prokaryotic cells are closest to what I want. Note that fungus cells share cell domains by not closing off cell walls to each other; this adds support to one thesis presented in this web page about the inside of the cell being closest to primeval life.

Code

Nucleus contains core of chromatic containing chromosones. Also has structure called nucleoli which have RNA.

Messenger RNA copy message off DNA and carry them out of nucleus to ribosomes. Transfer RNA assemble new proteins on surface of ribosomes; Transfer RNA bringing all kinds of amino-acids. Ribosome moves along mRNA building protein molecule.

(DNA separates and RNA nucleotides float in; once done the mRNA detaches, then ribosome walks the mRNA and legal tRNA's bind to it - the tRNA also containing the right one of 20 amino acids to link together; this can all happen in parallel with tRNA acting as translation scaffolding. The ribosome might be something like a zipper however; doing only part at once and feeding the mRNA in and the protein and mRNA out.)

Replication

DNA is a string pair with 4 node types; DNA